--- title: "Mount Sinai Brain Bank (MSBB)" id: "2378" type: "cohort" slug: "mount-sinai-brain-bank-msbb" published_at: "2021-02-24T00:32:18+00:00" modified_at: "2024-09-18T17:12:39+00:00" url: "https://dss.niagads.org/cohorts/mount-sinai-brain-bank-msbb/" markdown_url: "https://dss.niagads.org/cohorts/mount-sinai-brain-bank-msbb.md" excerpt: "Human brains were accessed from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB–Mount Sinai NIH Neurobiobank) cohort, which holds over 2,040 well-characterized brains. This cohort was assembled after applying stringent inclusion/exclusion criteria and represents the full spectrum of..." taxonomy_cohort_categories: - "ADSP" taxonomy_cohort_countries: - "United States of America" --- ## Description Human brains were accessed from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB–Mount Sinai NIH Neurobiobank) cohort, which holds over 2,040 well-characterized brains. This cohort was assembled after applying stringent inclusion/exclusion criteria and represents the full spectrum of cognitive and neuropathological disease severity in the absence of discernable non-AD neuropathology. For each sample, neuropathological assessment was performed according to the Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) protocol and included assessment by hematoxylin and eosin, modified Bielschowski, modified thioflavin S, and anti-β amyloid (4G8), anti-tau (AD2) and anti-ubiquitin. A Braak AD-staging score for progression of neurofibrillary neuropathology was assigned to each case. Quantitative data regarding the mean of the density of neuritic plaques in the middle frontal gyrus, orbital frontal cortex, superior temporal gyrus, inferior parietal cortex and calcarine cortex were also collected. Clinical dementia rating scale (CDR) was conducted for assessment of dementia and cognitive status. (Wang, M., Beckmann, N., Roussos, P. et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Sci Data 5, 180185 (2018). https://doi.org/10.1038/sdata.2018.185) ## Related Datasets - [NG00067 – ADSP Umbrella](https://dss.niagads.org/datasets/ng00067/) This dataset includes sequencing data and harmonized phenotypes from cohorts sequenced by the Alzheimer’s Disease Sequencing Project and other AD and Related Dementia’s studies. Samples are processed using a common… [Learn more](https://dss.niagads.org/datasets/ng00067/) - [NG00118 – AMP-AD SV WGS and SV-xQTL](https://dss.niagads.org/datasets/ng00118/) Structural variants (SVs) were discovered in 1,760 donors by running a combination of seven different tools to capture the main classes of variation, including deletions (DEL), duplications (DUP), insertions (INS),… [Learn more](https://dss.niagads.org/datasets/ng00118/) - [NG00196- Genotyping short tandem repeats using the ADSP R4 cohort](https://dss.niagads.org/datasets/ng00196/) A two-step pipeline was used to first identify expanded short tandem repeats (STRs) in ADSP samples using ExpansionHunter Denovo and then genotype the identified STRs, along with additional polymorphic STRs… [Learn more](https://dss.niagads.org/datasets/ng00196/) ## Related Studies - [sa000011 - Accelerating Medicines Partnership- Alzheimer’s Disease (AMP-AD)](https://dss.niagads.org/studies/sa000011/) The Accelerating Medicines Partnership- Alzheimer’s Disease Target Discovery and Preclinical Validation (AMP-AD) has supported the generation of whole genome data from three studies: the MAYO RNAseq Study, the Mount Sinai… [Learn more](https://dss.niagads.org/studies/sa000011/) - [sa000087 - Genotyping short tandem repeats using ADSP R4](https://dss.niagads.org/studies/sa000087/) Variation in tandem repeats (TRs), particularly large expansions of triplet repeats (e.g., polyCAG), is known to cause a number of late-onset neurological diseases. Due to their repetitive and degenerate nature,… [Learn more](https://dss.niagads.org/studies/sa000087/) - [sa000028 - Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain – Vialle et al. 2022](https://dss.niagads.org/studies/sa000028/) Structural variants (SVs), defined as any genomic rearrangements of 50 or more bp, are an important source of genetic diversity and have been linked to many diseases. Here, we report… [Learn more](https://dss.niagads.org/studies/sa000028/) ## Related Sample Sets - [snd10011 - AMP-AD WGS](https://dss.niagads.org/sample-sets/snd10011/) AMP-AD samples from the ROSMAP, MayoRNAseq, and Mount Sinai Brain Bank cohorts were whole-genome sequenced at New York Genome Center on the HiSeqX machine. FASTQ files were sent to GCAD… [Learn more](https://dss.niagads.org/sample-sets/snd10011/) - [snd10041 - AMP-AD WGS – SV Calls](https://dss.niagads.org/sample-sets/snd10041/) The AMP-AD WGS sampleset was sequenced on the Illumina HiSeqX sequencer (v2.5 chemistry) and made available from four aging and Alzheimer's disease cohorts: Religious Orders Study (ROS) and Memory and… [Learn more](https://dss.niagads.org/sample-sets/snd10041/) - [snd10147 - ADSP R4 Short Tandem Repeats (STRs)](https://dss.niagads.org/sample-sets/snd10147/) This dataset comprises short tandem repeat (STR) genotypes from 31,681 whole-genome sequencing (WGS) samples from the ADSP R4 data release. The STRs were genotyped using ExpansionHunter with a custom catalog… [Learn more](https://dss.niagads.org/sample-sets/snd10147/) ```